3.5 Nucleic Acids

Nucleic Acids

Nucleic acids store and transmit genetic information in all living organisms. DNA holds the instructions; RNA reads and carries out those instructions to build proteins. Understanding their structure explains how traits get passed from parent to offspring and how cells know which proteins to make.

Components of Nucleic Acids

Every nucleic acid is built from repeating units called nucleotides. Each nucleotide has three parts:

• Phosphate group — gives the molecule a negative charge and links nucleotides together along the backbone
• Five-carbon (pentose) sugar — forms the structural backbone of the strand
  • Deoxyribose is the sugar in DNA. It's missing a hydroxyl group ($-OH$) on the 2' carbon (hence "deoxy")
  • Ribose is the sugar in RNA. It keeps that 2' hydroxyl group, which makes RNA less chemically stable than DNA
• Nitrogenous base — the part that varies between nucleotides and determines base-pairing behavior

The nitrogenous bases fall into two categories based on their ring structure:

• Purines have a double-ring structure (a fused six-membered and five-membered ring)
  • Adenine (A) and Guanine (G)
• Pyrimidines have a single six-membered ring
  • Cytosine (C), Thymine (T) (DNA only), and Uracil (U) (RNA only)

A purine always pairs with a pyrimidine. In DNA: A pairs with T, and G pairs with C. In RNA: A pairs with U instead of T, and G still pairs with C.

There are two main types of nucleic acids:

• Deoxyribonucleic acid (DNA) — double-stranded; stores genetic information long-term
• Ribonucleic acid (RNA) — typically single-stranded; carries out various roles in gene expression

DNA Structure for Genetic Storage

DNA forms a double helix: two polynucleotide strands wound around each other. Several features of this structure matter:

• The two strands are antiparallel, meaning they run in opposite directions (one 5'→3', the other 3'→5'). The 5' end has a free phosphate group; the 3' end has a free hydroxyl group.
• Phosphodiester bonds link adjacent nucleotides along each strand, connecting the 3' carbon of one sugar to the 5' carbon of the next through a phosphate group. This creates the sugar-phosphate backbone.
• Hydrogen bonds between complementary bases hold the two strands together:
  • A–T pairs form two hydrogen bonds
  • G–C pairs form three hydrogen bonds (making G–C pairs slightly stronger)

Complementary base pairing is what makes DNA replication possible. Each strand acts as a template for building a new partner strand. This is called semiconservative replication because each new DNA molecule keeps one original strand and one newly synthesized strand.

DNA stores genetic information in the sequence of its bases. A gene is a specific stretch of DNA that encodes a protein or a functional RNA molecule. The order of nucleotides in a gene ultimately determines the amino acid sequence of the protein it encodes. The complete set of an organism's DNA is called its genome.

RNA Structure and Cellular Roles

RNA differs from DNA in a few key ways:

• Single-stranded (though it can fold back on itself to form hairpins and loops)
• Contains ribose instead of deoxyribose
• Uses uracil (U) in place of thymine (T)
• Generally shorter than DNA molecules

That single-stranded flexibility allows RNA to take on many different shapes and functions. The major types of RNA each play a distinct role:

Messenger RNA (mRNA) carries the genetic message from DNA to the ribosome. During transcription, a gene's DNA sequence is copied into mRNA. The mRNA sequence is read in three-nucleotide units called codons, each specifying a particular amino acid.

Transfer RNA (tRNA) is the adapter that matches codons to amino acids. Each tRNA has an anticodon (a three-base sequence that pairs with an mRNA codon) and carries the corresponding amino acid to the ribosome during translation.

Ribosomal RNA (rRNA) makes up the structural and catalytic core of the ribosome itself. rRNA actually catalyzes the formation of peptide bonds between amino acids, making the ribosome a ribozyme (an RNA molecule with enzymatic activity).

Small nuclear RNA (snRNA) helps process pre-mRNA by removing non-coding sequences called introns and joining the remaining coding sequences (exons) together. This splicing step produces mature mRNA ready for translation.

MicroRNA (miRNA) and small interfering RNA (siRNA) regulate gene expression after transcription. They bind to complementary sequences on target mRNA molecules and either block translation or trigger mRNA degradation, which fine-tunes how much protein gets made.

Nucleic Acid Metabolism and Information Flow

The central dogma of molecular biology describes the standard flow of genetic information:

$\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$

A few additional concepts tie into nucleic acid structure and function:

• Nucleases are enzymes that break phosphodiester bonds between nucleotides. They're essential for DNA repair, DNA replication (removing primers, for example), and RNA processing.
• Nucleosides are nucleotides without the phosphate group (just a base + sugar). They serve as precursors that get phosphorylated to form the nucleotides used in DNA and RNA synthesis.
• Base stacking interactions also stabilize the double helix. Adjacent base pairs stack on top of each other, and the hydrophobic interactions between these stacked rings contribute significantly to DNA's overall stability, alongside hydrogen bonding.